changeset 1:de51aa03c9b9 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427

--- a/computeMatrix.xml	Wed Dec 16 16:42:28 2015 -0500
+++ b/computeMatrix.xml	Fri Dec 18 08:01:48 2015 -0500
@@ -59,7 +59,7 @@
                 --sortRegions '$advancedOpt.sortRegions'
                 --sortUsing '$advancedOpt.sortUsing'
                 --averageTypeBins '$advancedOpt.averageTypeBins'
-                $advancedOpt.keepNAs
+                $advancedOpt.skipNAs
                 $advancedOpt.skipZeros
                 --binSize $advancedOpt.binSize
 
@@ -182,7 +182,12 @@
                     <option value="std">std</option>
                 </param>
 
-                <expand macro="keepNAs" />
+                <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
+                    label="Convert missing values to 0?."
+                    help="If set to 'yes', missing values (NAs) are converted to 0.
+                          The default is to ignore such cases, which will be
+                          depicted as black areas in the heatmap by default." />
+
                 <expand macro="skipZeros" />
 
                 <param name="minThreshold" type="float" optional="True"
@@ -219,7 +224,7 @@
             <param name="binSize" value="10" />
             <param name="sortUsing" value="sum" />
             <param name="averageTypeBins" value="sum" />
-            <param name="keepNAs" value="True" />
+            <param name="skipNAs" value="False" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
             <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />

--- a/deepTools_macros.xml	Wed Dec 16 16:42:28 2015 -0500
+++ b/deepTools_macros.xml	Fri Dec 18 08:01:48 2015 -0500
@@ -61,36 +61,6 @@
             </when>
         </conditional>
 
-<!--
-            $mode.advancedOpt.includeZeros
-
-
-        #if $plotTitle and str($plotTitle).strip() != "":
-            - -plotTitle '$plotTitle'
-        #end if
-
-
--->
-
-    <xml name="bigwigCorrelate_mode_actions">
-        <expand macro="region_limit_operation" />
-
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <expand macro="includeZeros" />
-                <expand macro="zMin_zMax" />
-                <expand macro="colorMap" />
-                <expand macro="plotTitle" />
-                <expand macro="plotNumbers" />
-            </when>
-        </conditional>
-    </xml>
-
     <xml name="includeZeros">
         <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
             label="Include zeros"
@@ -111,7 +81,7 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.5.11</token>
+    <token name="@WRAPPER_VERSION@">2.0.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
@@ -418,13 +388,17 @@
         </param>
     </xml>
 
-    <xml name="keepNAs">
-        <param argument="--keepNAs" type="boolean" truevalue="--keepNAs" falsevalue="" checked="False"
-            label="Treat missing data as zero"
-            help="If set, missing data (NAs) will be treated as zeros.
-                The default is to ignore missing data and not included
-                in the output file. Missing data is defined as those
-                bins for which no overlapping reads are found." />
+    <xml name="skipNAs">
+        <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
+            label="Ignore missing data?"
+            help="This parameter determines if non-covered regions
+                 (regions without overlapping reads) in a bam/bigWig file
+                 should be skipped. The default is to treat those
+                 regions as having a value of zero. The decision to
+                 skip non-covered regions depends on the interpretation
+                 of the data. Non-covered regions may represent for
+                 example repetitive regions that want to be skipped.
+                 (default: False)" />
     </xml>
 
     <xml name="input_save_matrix_values">